I don't know exactly how things go on this platform because my truck has ever seen a dealer aside from recall work, but like everything else in life it is nuanced.
Folks get away with honored warranties while tuned this way or that, so the narrative that some method is "untraceable" gets out. Others get busted, and so that method must not be so covert.
Folks on this thread have so much more direct involvement I would trust that before any community anecdotes.
On Volkswagen AG tuning, it seems there is really nothing a dealer can see as to past tuning.
So if a repair can be decided at the dealer level, then all is good.
But some work/coverage requires getting VAG corporate engineers involved, and folks believe VAG can find some forensic clues to a prior tune if cooperate engineers really want to dive in deep, and that's the other nuance - usually they don't go too deep.
E.g. replacing a 2.0 I4 that goes into every mainstream product - probably not.
Replacing an expensive 4.0 TT V8 in the high end stuff - probably a little more diligence.
it's hit and miss, and so many fringe cases.
Best just to go in with your big boy pants cinched tight.